Hey Phillip,
So I've tested it out on my side and it seems to be working now. If you make an overpayment, you will be prompted with a message asking if you want to overpay. Once the payment is saved, it's pushed to QB then QB sends back the data for credits.
In order to see the credits you need to make sure that QB is open so it can sync. If QB is not open, then you will not get to see the credits until the next time the sync engine runs.